Spoiler warning: this article may contain major plot or ending details.
When Ben/Summer was captured by the Pinchers, blindfolded and disorientated, he/she placed a tracking device in the submarine so that when rescued, the Rangers can retrace their steps to find the Pinchers's hideout. Later, returning with the player, Ben and Summer explored the submarine, rescuing several of Ukulele Pichu's friends from Dolce Island. After losing to Ben and Summer at the helm of the submarine, Blue Eyes crashed it on the seafloor in anger. She later gets in trouble for this. Ben and Summer had ten minutes to escape the submarine, and rescue Blue Eyes, two Pincher grunts and some of the Dolce Island Pichu that hadn't managed to get away before along the way.
This article is part of both Project Locations and Project Sidegames, Bulbapedia projects that, together, aim to write comprehensive articles on every location in the Pokémon world and the Pokémon Sidegames, respectively.